Metroid: A long journey backward
by Vaekrix
Summary: After the events on Tallon IV, Samus gets a message from a Federation Admiral. There is a link between the Space Pirates and a race called the Covenant, which existed back before Earth was drained and left. Now Samus must go back to destroy this link.
1. The Admiral's Message

Once again Samus Aran had cheated death, escaped it by mere inches. As her ship sped away from the planet below, Tallon IV, she knew that, like all of her other missions, she would never forget this one. As she slowed the ship down, Samus relaxed in her chair and ran a diagnostics check on her suit. Sure, it would accomadate various upgrades if they proved safe, but the whole business of being stripped of upgrades, such as the experience she had had in the Pirate Frigate before landing on the planet, seemed to be dangerous. The suit gave an all-clear, however, with only the Phazon modifications missing from the design. Samus vaguely wondered what would happen with the Metroid Prime now. She had left in a hurry, and hadn't taken care to ensure it was really gone for good. Just as she was considering the option of going back down to check on things, however, her communications device beeped. Thumbing the button on the console in front of her, she saw a man's face appear on the screen in front of her. He looked vaguely familiar, and wore a broad grin.

"Samus Aran... I'm glad I could reach you. I'm Fleet Admiral Correlon, in case you've forgotten," the man spoke, in a deep, booming voice. Samus had to think for a moment before the name registered.

"Oh... yes," she smiled faintly. Any news from Correlon was often not pleasant, but he seemed downright jovial about something.

"Miss Aran, I think you'll be very, very pleased indeed to hear the news I have for you," the Admiral said.

"By all means then..."

"Well, as you know, the Space Pirate threat has grown to be a major problem for the Federation." _Yeah, _Samus thought, _I'm pretty sure I'm well aware of that._ "We, that is to say, my science team here at the Federation outpost near Zebes, have developed something you should find highly pleasing. If you'd just come on by, we can show it to-"

"Sir, I have just been through, yet again, an exhausting ordeal. This will have to wait..."

"No! No! It can't wait, you see? It must happen quickly, before more problems arise."

"What are you talking about, sir?!" Samus was growing impatient, she wished that the Admiral would be slightly less cryptic about things, seeing as this link was already encrypted.

"Can't talk about it on this, we have to meet in person. Too much risk of this being picked up," Correlon said, looking around nervously as if the possible interceptors were in the room with him.

"Even if you don't talk about "it", whoever may or may not pick this up knows where you are," Samus said irritably.

"Look... just come by the outpost, and we'll discuss it here," Correlon's jovial attitude had been replaced with a grumpy one at this point.

"Sure, okay, whatever." Samus jammed the button to close the link, wishing she had ignored it to begin with. She was technically a freelance bounty hunter, she didn't _have_ to follow orders from the Federation. Whatever Admiral Correlon was so eager about, though, Samus figured she ought to go see for herself.

"Computer, you have the coordinates to that outpost, yes?"

"Affirmative," the ship replied in a brass, robotic tone.

"Jump to hyperspace, take us there," Samus ordered. As the ship swivelled in the correct direction, Samus braced herself.

The ship came back into normal space, and Samus looked out at the outpost through the front viewing "windows". It was a rather small thing, to say the least. What could possibly be so important that could fit on something that small? Samus expected a weapon or something. Then again, even if it were a weapon, size was no measure of power. Her arm cannon was proof of that, since it could do more damage than most larger weaponry.

"This is Federation Outpost 1092-H-Zebes, hailing unknown craft. Please respond immediately, or more drastic measures will be taken." The voice came from the same communication device Samus had spoken with the Admiral on, though this was voice only. _Unknown craft? Don't they have the technology to detect their own ships? _Then Samus realized that she was still partially cloaked, which explained it.

"This is Samus Aran, here by orders from Fleet Admiral Correlon."

"Please disengage all cloaking devices so that we may verify."

"Right," Samus thumbed the button to disable the cloak. She doubted the station had the means to take her ship in a battle anyway, if it came to that.

"Verified, you're clear for docking. A maintenance team will meet you there to inspect and, if necessary, repair your ship." Samus instructed the ship to dock with the station, and it moved to comply. After about five minutes, there was a dull clunk as the ship was secured to the station. Samus got out of her chair and went to get out, securing her helmet back on as she did so. Predictably, there were about four armed men waiting just outside the ship, with the small group of maintenance officers waiting behind them. One of the men turned and nodded to the man next to them, and they both motioned for Samus to come down. There was a small bit of gravity here on the dock, so Samus leapt away from the ship, and landed lightly in front of the men. They then turned away and began walking past the maintenance team, and Samus followed. They went through an airlock door, and waited a moment as the door shut behind them and the room pressurized. As soon as it was, the door in front opened, and the four men removed their helmets.

"Howdy, Miss Aran," the one nearest Samus said, mispronouncing her name horribly. Samus nodded and removed her own helmet, and some of the mens' faces showed shock. Samus knew they expected a he-woman of sorts, as did most who knew her reputation and also knew she was female. The ones who didn't always thought she was male. Hastening to conceal their shock, the men turned away and led the way down the hall behind them. At the end was an elevator. It was a rather tight fit, with all five of them in their suits, but they managed. At least there was none of the awkwardness of packing an elevator full of usual people. Here, the armor just touched, not skin or anything. The elevator went down, and opened to a small white room.

"Decontamination chamber," one of the men explained, in a voice mercifully free of an odd accent, unlike the other man. The group stepped into the room, and waiting as it went through it's process, then a pair of doors slid open into a wide, open, white room, where a number of people dressed in white lab coats were gathered around some sort of machine at the center of it. A number of cables as thick as Samus' body extended from the walls to the machine. The only man not in a lab coat, other than the four with Samus of course, was a very tall, very large man. He looked over his shoulder at Samus and smiled broadly.

"Samus Aran, we meet in person at last," he said loudly, his booming voice causing several of the scientists to jump. He took long strides as he approached Samus and extended his hand.

"Admiral," Samus said, returning a wan smile as she shook his hand. The Admiral looked down at her hand and smiled, if possible, more broadly.

"And the famous Chozo suit... I envy you," he said, examining the suit with hungry interest. Samus, eager to both get to the point, and to get the subject off of her suit, gestured to the machine behind Correlon.

"This is what you wanted to show me, yes?" she asked, jerking the Admiral's eyes away from the Chozo arm cannon.

"Yes, yes, this is indeed," he said, leading Samus away from the four men who had escorted her there, who excused themselves from the room at that point.

"What is it?"

"A true marvel of modern science, that's what it is. We've invested several trillion credits into this project, as well as nearly two decades of work. Mind you, I only joined when it was moved to this outpost a few years ago..."

"Why the move?"

"Well, to be closer to you, of course. It was, after all, intended for your use. At the time, you were working on Zebes, of course, but we figured your excursion to Tallon IV would be temporary, and that you'd be back, so we didn't bother to try a move out there next."

"Yeah, it's so much harder to fly here in my ship. You guys should've moved it," Samus said sarcastically, making the Admiral laugh, "but you still haven't told me _what_ this thing is, and what it does."

"Plain and simple, it's a time machine," this comment made Samus laugh, "no, seriously. It's intended for time travel. You see, the Space Pirate's have been traced back to another race that terrorized what was formerly a human planet. I'm sure you've heard of Earth? It's a desert now, of course. Consumed of all resources and left behind.Yes, a race that called themselves the Covenant were in conflict with mankind many years ago. They eventually, over the course of many, many years, came to be modern Space Pirates. We're not sure how, since there are many differences between the two, biologically, but we're sure that they're the same, just changed."

"And why send me back? I could simply destroy the Space Pirates in this time period, probably with less hassle, and less..." Samus regarded the machine apprehensively, "... risks."

"Well, the thing about the Covenant is, we nearly destroyed them. Unlike the Space Pirates, we pretty much knew where all of them were, they weren't spread throughout the universe. If you go back, you'll certainly be more powerful than anyone that they had at the time. You'll want to meet up with a man there, who seems to have been the Samus Aran of the time. He was called the Master Chief, and according to our records, he was the main destructive force behind the war with the Covenant. I can't see why, he was part of a project called the Spartan-II project, along with quite a few other people. All of the others, as far as we know, died. We can only guess how he survived where the others couldn't."

"So kind of like if there were twenty others just like me, and they all die in the same kind of combat as I've been through, yet I survive?"

"Yeah, sorta..."

"So when am I supposed to go on this little venture?"

"As soon as we get this up and running. There's about a twelve hour charge time..."

"Oh, good, enough time to pack and grab a bite to eat," Samus said. The Admiral laughed at this.

"Yes, I'm sure. You won't need anything other than yourself and that remarkable suit, but eating wouldn't be a bad idea after what you've been through."

"Myself and my remarkable suit? I don't get any credit, it's always the suit," Samus said, in mock anger. Again, the Admiral laughed.

"Well, get a bite to eat, get some rest, and I'll see you in about thirteen hours. Last minute diagnostics and such, you know..."


	2. Never Fear, Samus Is Here!

In response to a review about the clicheness of time travel: I kinda figured it would be a little cliche, but I thought it would make more sense than Samus happening to stumble upon Master Chief. Besides, it seemed logical to me that Earth has been either destroyed or drained and abandoned by the time Metroid 1 occurs, since it pretty much doesn't exist anymore, so it made sense that Samus had to travel back through time.

As for what's happening. This is occuring in the period of time almost just after Halo 2 ends. I've started at the place where the ship Master Chief stowed away on has landed on Earth, and, according to the official Halo Uprising comics that will bridge the gap between Halo 2 and 3, he's captured for interrogation. It'll be a while before the next chapter is out, because I have to play through Halo 1 and 2 again for some background before I start making up events for 3. When the game comes out, it will undoubtedly make things easier.

Thanks to all those who like the work. This is my first work being read by others, so I'm glad it seems to be going so well.

* * *

After an hour of last minute checking of the machine, and then the twelve hour warm up, Samus stood in front of it, slightly worried.

"Now, we won't be able to pinpoint the exact location of Master Chief with this, but we will be able to get you within about a fifty mile range. Chances are, he'll probably be with others, but we can't be sure. Just make sure you don't make any significant movements, since theories are that it'll tear you apart if you do. Also, though this should be obvious, don't fire your weapons in there! We have no theories, but we know it's not a good idea, which is, again, obvious. Lastly, you'll have to shut off the suit while you're inside, and I mean completely. This thing will fry the systems if they're online. Well, I guess that's all, good luck then," the Admiral explained to Samus. After he had finished, he clapped Samus on the back and left the room, along with many other scientists. One scientist stayed behind at a control panel a few feet from the machine, armored like the soldiers who had escorted Samus in.

"Ready?" he asked, his tone anxious and worried. Samus nodded and approached the machine, which was basically a cylinder with a door that slid apart for entry, which did open as Samus stepped toward it. Forcing away fear, she stepped into the cylinder and the doors shut. Acting quickly, since the scientist outside could activate the machine at any time, Samus shut off her suit and felt the weight of it press upon her. Suddenly, and unexpectedly, a bolt of what felt like electric bolt shot through Samus's body. Disoriented, half blind, and mentally numbed by the shock, Samus suddenly found herself in the dark and weightless, which didn't help with the disorientation. In the next second, a blinding white light shone through the darkness and engulfed her. She stopped herself from shielding her eyes just in time, remembering that she shouldn't move. Finally, Samus felt gravity come back, along with a falling sensation, and hit solid ground with a ground shaking thud. A blinding light still filled her vision, and the first thing she did was slip down her visor, which had been up so that she could see when the suit was powered down. Pain seared through Samus, particularly at the spine, because her suit hadn't been able to protect her as much as if the shields had been active when she fell. Groaning, she forced herself up, as the suit began to start back up. When her HUD finally showed up on the visor, she looked at her surroundings curiously. It was, Samus suspected, a rainforest; lush, green, and beautiful. The sight was slightly marred, however, by the sight of dead bodies littering the ground and treetops. They were alien, and Samus could see a slight resemblance between them and the Space Pirates. If this Master Chief really was the Samus Aran of the time, this had to have been his work.

"Follow the bodies," Samus said to herself, judging which way this Master Cheif ought to have gone. Most of the bodies lay on their back, heads facing North-East, so Samus headed that way. The forest was dense, unyielding, and fierce with all manner of spiny and pokey plants that would be sure to rip bare flesh, but merely burned to ash as they touched the suit's shielding. Here and there, paths had been torn open by weapons fire, and as the bodies grew less frequent, these paths were what Samus was forced to follow instead. After about fifteen minutes of walking, Samus heard speaking in the distance. It was an old Earth language, some sort of derivative of English, Samus suspected, which had been the Earth's universal language at one point. The voices were odd, though, not quite human. Grunting, rasping voices that didn't sound quite human at all. Then another voice, more human, yet deep and robotic sounding, spoke up.

"I have nothing to say to you. Kill me or leave me..." the voice said. As Samus passed through the next opening in the dense rainforest, a ship came into view, seeming to slowly expand as Samus's view became less impeded. It was huge, as big as many of the largest flagships of the Federation. It also held a majestic, alien beauty, unlike Samus had ever seen before. If Samus were not sure that the aliens would not be too welcome of it, she would have liked to explore the vessel. A large cracking sound brought her back to her senses. In front of the ship, there was a man, or perhaps a woman, chained to a chair. He or she was wearing a suit much like Samus's own, and was surrounded by about twenty of the alien beings. One of them had just rammed the butt of a rifle into the armored figure's stomach.

"We do not play with you, Demon. Give us the information we want now, or you will regret it!" Samus's suit was barely able to translate, as the aliens' voices butchered the language so badly. The one speaking to Master Chief turned away, and suddenly spotted Samus standing there. Both thinking fast, and scolding herself for being stupid enough to stand in the open, she took off running straight at the alien before he could alert his fellows. He was a large one, but when Samus raised her arm cannon and launched a pair of missles at his chest, he fell back, apparently dead.

"Well, this will be easy," Samus muttered, taking aim at the next one. He was ready, though, and fired a large cannon. The grenades it launched bounced and hit Samus hard, draining a whole energy tank. She retaliated with another pair of missles, but this one managed to stand his ground, and charged straight at Samus. Already, the others were readying themselves, levelling their own grenade launchers. Samus leapt backward, narrowly avoiding the grenades as ten of the large aliens fired at once. She switched over to her ice beam and charged it up, then fired the ice spreader into the main group. Six were frozen, and another missle shattered them all. The Master Chief was simply sitting there, unnoticed by any of them, watching idly as the fight continued. Noticing this, Samus fired a missle near the other aliens, and they leapt backward to avoid it. She ran at Master Chief, realizing as she went that he was bound by energy chains rather than ordinary ones. She switched to the wave beam and fired at the chains a few times before it flickered and Master Chief managed to break away from them. Not hesitating for a moment, he grabbed up one of the dead aliens' grenade launchers, and turned on the others. Together, Samus and Master Chief made easy work of the rest of the aliens.

"You alright?" Samus asked when they were done, as she sat on the ground.

"Fine," Master Chief said, as he took a seat as well, back in the chair he had been previously chained to.

"You're the Master Chief?" The armored man simply nodded. After a long pause, Samus decided that Master Chief wasn't in the mood for chatting, and laid back on the soft grass. Though she tried to resist, it was comforting to be resting for the first time since her problems on Tallon IV. She soon fell unwillingly to sleep.


	3. I Want Answers

Sorry for having taken so long to write up a new chapter, but I've been moving, and I didn't get any time for writing during the move.

As someone said in the reviews, chatty Master Chief is bad, which I completely agree with. Unfortunately, I had to have him talk a bit in this, but no more than he had to to get answers. Plus, when I use John's point of view, I'm mostly using the personality portrayed in the Halo novels, to avoid a crappy John personality.

* * *

"I have nothing to say to you. Kill me or leave me..." John remembered saying. He knew the drill, and "spilling the beans", so to speak, was not an option. If they decided to kill him, well... that was that. It would be in other hands to save Earth. Instead, the Brute rammed his rifle into John's abdomen, and his breath left him in a rush. 

"We do not play with you, Demon. Give us the information we want now, or you will regret it!" the same Brute spat angrily. Under the visor, John merely smiled weakly, knowing that the patience of his new friends was wearing thin. The Brute turned away, growling with rage, then stopped suddenly. He was staring off the way the Brute's had dragged their captive, with a look of disbelief plastered on his face. John looked up, too, and saw a figure standing there, clad in some strange armor in purple, yellow, and red colors. The armored figure noticed this, and sped forward, levelling a strange weapon at the Brute who had been interrogating John. A pair of what appeared to be missles launched from the weapon and killed the Brute instantly. John was pleasantly surprised at the weapon's firepower, and at the same time slightly wary. It wasn't a human weapon, which meant it could only be Covenant technology. The person was firing on the Covenant, though, so maybe it wasn't? Either way, things were working out well for John, for the time being. The soldier fired an impressive spray of ice, which froze a majority of the Brutes on the spot, so that a single missle shattered them all like glass. The figure seemed to notice John then, and ran toward him, levelling her cannon now at him. _Great, out of the oven and into the fire, or however that saying goes, _John thought, as he closed his eyes in preparation for death. Instead, streams of electrical energy streamed from the weapon and the chains binding John weakened. Siezing the opportunity, and marking the armored soldier as a temporary ally, John threw the chains open. Not even hesitating to gain his bearings, John stooped down and grabbed one of the Brute Shots, then began firing on the rest of the Brutes alongside his new ally. In only a minute more, the rest of the Brutes lay dead on the ground. The other soldier, panting visibly, sat gently on the ground. Well, it wasn't a threat. That was a comforting though for John.

"You alright?" a distinctly female voice issued from within the other's helmet.

"Fine," John replied simply, taking a seat as well. He was tired, and a bit sore, but still on full alert.

"You're the Master Chief?" the woman asked, startling John. How did she know who he was? Was she a new breed of Spartan, sent to aid him? Surely not, or would John not have recieved the same new weapon? Maybe it was only compatible with this new suit, which could only be used by this new Spartan type, who knew? Not in the mood for introductions, and not caring who this person was at the moment, John just nodded. The woman, satisfied, lay back and apparently fell asleep. _Stupid, careless, falling asleep here of all places, _John thought, scowling. Maybe she figured John would keep watch, trusted that he was an ally and that he would risk his life to protect her as she had done for him. That was even more stupid. Maybe this new Spartan, or whatever she was, was significantly less intelligent than the Spartan-II soldiers. Oh well, this new person wasn't a friend, wasn't even an aquantaince, and John wouldn't waste his time helping patch up her faults. Either the woman would keep up or she wouldn't.

After about half and hour, John was satisfied that the woman was asleep, and leaned foward to remove her helmet. Time to find out who this was. As he pulled off the helmet, long blonde hair fell out, and the woman's sleeping face came into view. John might've called her beautiful, if he knew such a thing. She certainly looked well for what John supposed was a hardened soldier, judging by her impressive performance. Replacing the helmet, and judging that she was more than likely not a Spartan, John focused his attention to the more interesting thing in the woman's possession. The pure destruction encased in gleaming metal, which John wondered if it was attached to the arm or not.

_Not,_ John thought, as the cannon slid easily off of the woman's arm. Raising it to eye level, John examined the sleek exterior of the weapon. It was completely smooth, and nothing like a clip for reloading or anything protruded from it. Evidently, everything the woman needed was inside the cannon. John peered into the interior and saw a series of switches and buttons, probably for changing between the different weapon modes. Where, though, was everything that powered it? The ammunition, the batteries, anything that might've provided the cannon's destructive power. More importantly, where was the arsenal of missles stored? This definitely wasn't human technology, and it made John suspicious. He stood up and bent down near the woman's head, and began to knock on the visor. Sleep time was over, time for some answers.

* * *

_Relax, Samus, relax, _Samus told herself, laying there on the ground. Her suit's sensitive sensors had woken her up only moments after drifting off to sleep. What she needed to do was relax her mind so that her neural interface would shut down. Taking deep breaths, Samus felt some of the tension of the previous battle ebbing away. The sensations that the suit was simulating went away, and again Samus sunk into sleep.

_Clink. Clink. Clink._

Samus lay on the ground, slightly annoyed by the noise. Who was tapping on her visor, and why? _Leave me alone, _she said silently, as the rythmic tapping persisted. It was peaceful to be laying on the soft grass. The tapping didn't stop. Conceding that she'd have to get up to stop the person, Samus opened her eyes and sat up, bringing her arm cannon up as she did so. Except that it wasn't on her arm. Looking up, she saw Master Chief standing over her, holding the cannon in his hands.

"Where did you get this?" he asked, in what Samus recognized as a threatening tone.

"I...why?" Samus replied evasively.

"This looks like alien technology. Where did you get this?" Master Chief's tone became angry, and it took Samus a moment to figure out why. The man must have thought that Samus was one of those aliens, the Covenant. Why would he think that, though? Hadn't Samus just killed Master Chief's captors?

"It's alien technology, yes, Chozo made. It's not something from those others," Samus gestured toward the dead aliens lying on the ground. The Master Chief looked at the cannon, then back at Samus, and shook his head. He obviously wasn't convinced.

"Who are you?" he asked, the rage gone but the voice still threatening. Samus moved to get up, but thought better of it and stayed put.

"Samus Aran, bounty hunter. I was sent here by-"

"Bounty hunter?" Master Chief asked, sounding as if this were no better than being a Covenant leader.

"Yes, I-"

"Who sent you?" Master Chief interrupted again.

"Admiral Correlon, he's part of the Galactic Federation, and-"

"Federation?" another interruption from the Chief. Samus sighed, feeling this wasn't going too well.

"I don't have the time to explain right now. Just accept that I'm your ally, and I'm here to help. Answers will come eventually," Samus said, driving through any interruption the other may have. Master Chief stood still for a moment, then tossed the arm cannon to Samus, who caught it and slipped it back on.

"Time to sleep, not to explain?" Master Chief said questionably. He left it at that, though, as he began to walk away. Samus leapt up from the ground and went to follow him.

* * *

Thanks to Lunatic Pandora for pointing out the problem with Samus not realizing that Master Chief was removing her armor. I did my best at a quick fix for the problem. As for the fact that her arm cannon was easy to pull off, I've always been under the impression that her fingers curl around the end, since it kinda looks that way with the X-ray visor in Metroid Prime. 


End file.
